


A Phoenix Rises

by WillSherJohnKhan



Category: Sherlock (TV), Star Trek Into Darkness - Fandom
Genre: Alternate Universe, F/M, Uneasy Alliance
Language: English
Status: Completed
Published: 2014-10-26
Updated: 2016-02-06
Packaged: 2018-02-22 16:27:58
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 12
Words: 8,242
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/2514323
Author URL: https://archiveofourown.org/users/WillSherJohnKhan/pseuds/WillSherJohnKhan
Summary: <blockquote class="userstuff">
              <p>When the Earth is threatened, sworn enemies must work together to defeat a greater foe.</p><p>Disclaimer:<br/>I don't own any of these characters. I just like to play with them every now and then.</p>
            </blockquote>





	1. Prologue

*** 

Captain’s Log, Stardate: 2261.87

In an attempt to rectify their error in judgment when appointing Alexander Marcus as the head of Starfleet, the Federation now placed their faith in Admiral Patrick Oswald.

Oswald was not the type to allow fear to get the better of him. Nor would he act first and suffer the consequences later. He offered Starfleet a calm, thoughtful and well measured approach to dealing with any and all situations.

As to whether he would make a better leader was still to be determined. Even as he took office, concerns were being raised.

Though all agreed that Starfleet didn’t need another Admiral Marcus, Oswald’s open armed approach to dealing with the increasing number of alien races the Federation was encountering was making many uneasy.

It was all very well offering the hand of friendship. But it was felt that it should only be done once it had been determined with absolute certainty that those being offered friendship were genuine, and did not have any hidden agenda’s or ulterior motives.

Initially Oswald’s policy seemed to work well, and everyone began to feel more at ease with his more moderate approach.

And then these policies were spread far and wide and into deep, deep space.

It was here that they caught the attention of a race of beings that were not interested in friendship, peace or even war.

They believed in only one purpose – assimilation.

Capt. James T. Kirk

***


	2. Desperate Times, Desperate Measures

***

Starfleet Headquarters – San Francisco

The first anyone knew of their existence was when the peace was violently shattered by a sonic boom as the solitary cube-shaped vessel breached the Earth’s atmosphere.

Shock, surprise and curiosity were quickly replaced with terror and panic as the new arrival made its intentions clear as the ship started firing indiscriminately.

***

The air was soon thick with smoke and debris as buildings toppled under the relentless onslaught.

There were fires in every direction. The acrid smell of burnt bodies wafted on the breeze.

And all the while, explosions and the constant scream of sirens battled for supremacy.

***

James T. Kirk fought his way through the chaos as the population stampeded en mass in a desperate attempt to get to safety.

But Kirk was headed in the other direction.

He didn’t have a plan in mind as such. He just knew that this threat, whoever they were, needed to be dealt with.

For that he was going to need the assistance of one particular individual. Unfortunately it was impossible to reach him by using his communicator.

***

“Did you find them?” Kirk asked as he made his way through the now abandoned warehouse.

Hikaru Sulu looked up from the manifest he was reading. “Yes Captain,” he replied, indicating vaguely in the area to what the Captain sought.

Kirk noted the grim expression on the lieutenant’s face. “Is there a problem Mr Sulu?”

“Yes Captain,” he paused briefly before continuing. “Where there should be 73 cryotubes, there is now only one.”

He then entered a code from the manifest into the terminal in front of him.

As soon as the code was entered, a concealed draw that was located in the wall gracefully opened.

Inside the draw was the remaining cryotube. Its inmate still blissfully unaware of what was happening on Earth at that very moment, nor the role that he would be asked to play to save the planet and its inhabitants.

“Captain, I feel it is my duty to point out…”

“I know what you’re going to say Mr Spock,” Kirk said as he turned to his Vulcan First Officer. “Unfortunately there is no time to debate the issue. Like it or not we need Khan, his intellect and his expertise with weapons.”

Kirk then turned back to Sulu. “Download all the data from the terminal about the missing cryotubes. It may give us a clue as to where they have been moved to.”

Sulu nodded and began to do as ordered.

“Captain,” Spock began.

Kirk spun around. “No Spock. I will not be accused of being another Alexander Marcus. We get all the information we can, and when this situation is over we give it to Khan. He can then decide what he wants to do with it.”

He then flipped open his communicator. “Scotty, four to beam up.”

***

**Notes for the Chapter:**

> I hope you're enjoying this story so far. This is very much a work in progress, but the more I write, the better I can see where its heading.


	3. A Deal With the Devil

**Summary for the Chapter:**

> Disclaimer: I don't own any of these characters. I just like to play with them every now and then.

***

USS Enterprise NCC-1701

Medical Bay

“There’s no time to debate this. We have to do it now,” Kirk stated firmly.

He, Spock, Doctor’s Leonard McCoy and Carol Marcus were all standing around the as yet unopened cryotube.

“Have you forgotten what he did the last time?” McCoy demanded.

“Of course not,” Kirk responded, determined to keep his cool. He understood everyone’s concerns about what he was proposing they do. But if the reports he had begun receiving from the other Starfleet vessels that had attempted to engage the alien ship, it was becoming crystal clear that they were going to need something special if they wanted to survive the encounter.

He didn’t like no win scenarios, nor did he like losing. And he would not send his crew on a suicide mission.

So, if they were to have any chance of success, then they were going to have to rely on the skills of Khan Noonien Singh.

“He will not trust us,” Spock pointed out.

“I know,” Kirk replied.

“What do you have in mind?” Carol asked.

Before he could respond Ensign Molly Hooper came into the Medical Bay and made her way over to the captain.

“You wanted to see me Captain?”

“Yes Ensign. Your assistance is needed with a task we are about to perform.”

The young ensign looked over at the cryotube. When she saw who was within she unconsciously started to worry her lower lip with her teeth.

“Yes Captain,” she responded quietly.

Doctor McCoy pulled the Captain to one side. “Have you lost your mind?” He knew his friend well enough that he had an idea of what Kirk intended. “Goddamn it Jim, you’re playing with a girl’s life.”

“Bones, if there is one thing at this moment that I’m certain about is that Khan will not hurt so much as a hair on her head.”

“How much are you willing to bet?”

“Stop worrying,” Kirk said with confidence, trying to allay the doctor’s concerns. “Molly is the best person to keep Khan in line.”

“I beg to differ,” McCoy argued.

“She is, believe me. Don’t you remember? From the first time he came aboard this ship, whenever he got a glimpse of her he couldn’t keep his eyes off her. And whenever she was around he was more willing to behave.”

The doctor still wasn’t totally convinced. But even he had to acknowledge that the reality was they were going to need the Augments full and willing co-operation.

So, as crazy as the Captain’s logic sounded, it might actually work.

“All right,” he reluctantly agreed. “Lets get this over and done with.”

***

It felt like his eyelids were made of lead. But as soon as his internal organs started working again, he wanted to see exactly where he was.

Memories from the last time he’d been awoken overwhelmed him: Admiral Marcus, Section 31, designing weapons and ships, betrayal, revenge, the Klingon Homeworld, the Enterprise, Kirk, the death of his crew, crashing the Vengeance into Starfleet Headquarters, his trial and then oblivion once again.

“Its all right,” her soft voice assured him. “Try to take even, shallow breaths. That’s right, you’re doing fine.” And then he felt her small, delicate fingers as she gently ran them over his forehead and into his hair.

His eyes opened, then shut, the brightness of the room almost blinding. He opened his eyes again, looking right into the face of the young woman who had haunted his dreams.

 

The Bridge

“Nice and steady Mr Sulu,” Kirk instructed his helmsman.

“Aye Captain,” Sulu responded as the Enterprise navigated its way through the debris of other Starfleet ships.

“Onscreen.”

On the bridges view screen there appeared the enormous cube ship. 

Kirk turned in his chair to check with his Communications Officer. “Any response?”

Uhura shook her head. “No Captain. They’re not responding to our hails on any frequency.”

The Captain now turned to his First Officer. “Your thoughts Mr Spock.”

“They do not respond to our hails because they do not understand. Or because they choose not to.”

Kirk nodded in agreement.

The first option was a possibility, given that as far as he was aware the Federation had not come into contact with any beings with a ship such as this.

The second option had him on edge. If they could understand their hails but choose to ignore them, indicated that they were confident that they were the one’s in control of the situation, and they saw themselves as superior.

“Slow to impulse,” he ordered. “Shields up.”

“Yes Captain.”

Having announced its presence by raining destruction down on Starfleet Headquarters, and then destroying the ships that had tried to intercept it once it had retreated back to open space. The cube ship had then come to a complete stop, and waited.

“What are they waiting for? An invitation?” asked Ensign Paval Chekov, frustration and confusion colouring his words.

“Scan the ship Mr Sulu.”

“Aye Captain. Scanning.”

The turbo lift to the bridge opened to reveal Ensign Hooper and Khan Noonien Singh, who was once again dressed in his signature black Starfleet uniform.

“Permission to come on the bridge Captain,” he requested calmly.

“Permission granted,” Kirk replied.

Kirk turned back to the view screen. “Problem Mr Sulu?”

Sulu was busy checking, then rechecking the information that had come up on his terminal. “The readings we’re getting from that ship Captain. It doesn’t make any sense.”

“Explain?”

Sulu frowned as he re-read what was on his screen. “Its like nothing I’ve ever seen before.”

Something in the Lieutenants tone caught Khan’s attention, and with a nod from the captain, he walked over to view the readouts for himself. And what he read astounded him. “That’s not possible.”

Sulu read the scanners findings aloud. “There is no bridge, or a command centre, no engineering section. And there appear to be no crew quarters.”

“What about life signs?” Kirk asked.

“There doesn’t appear to be any signs of life.”

“Shields? Weapons?” Spock queried.

“There are no shields and no weapons.”

“Impossible,” Kirk exclaimed. “They just devastated San Francisco. How could they do that with no weapons?” 

He turned to Khan for his thoughts, but the augment looked as baffled as everyone else.

“It makes no sense whatsoever,” Khan stated, before turning back to look again at the findings. Then almost to himself he noted. “Their ability to limit the Enterprise’s scanners from being able to read anything about their ship would suggest some form of advanced technology.”

“Agreed,” Spock concurred.

Uhura cut in. “Captain, we’re being hailed.”

“Onscreen.”

The view of the cube vessel disappeared and what took its place took everyone on the bridge by surprise.

All they could see was a mass of compartments, in each there appeared to be two humanoid beings, all completely motionless. That was all the ship seemed to be made up of, rows and rows of compartments. They covered what appeared to be an unlimited number of decks. As to number, it was difficult to tell, tens of thousands, hundreds of thousands, possibly millions of individuals on one ship.

Kirk got up from his chair and took a step towards the view screen.

“I am Captain James T. Kirk of the Federation Starship USS Enterprise…”

There was an abrupt interruption from the other ship.

“We are the Borg. Lower your shields and surrender your ship. Your biological and technological distinctiveness will be added to our own. Resistance is futile.”

As abruptly as the transmission started, it ended.

Kirk turned to judge the reaction of his crew. Most looked as stunned as he, others were showing traces of fear. Then he turned to Khan.

The expression on the augments face was one of undisguised distaste.

Khan exchanged a look with Molly, who nodded her head encouragingly. He walked over to the Captain, his right hand outstretched.

“I refuse to give up that which makes me individual Captain. So I will help you in any way I can to defeat these…Borg.”

Kirk shook the augments hand firmly. “Welcome aboard.”

***

**Notes for the Chapter:**

> Well that was the easy part of the story written. Now to get on with the rest. I at least have worked out how the story will end. So the only thing I have to work out is what I need to do to get there. :-) I hope you have been enjoying the story so far.:-)


	4. Intruder Alert

**Summary for the Chapter:**

> When the Earth is threatened, sworn enemies must work together to defeat a greater foe.
> 
> Disclaimer: I don’t own any of these characters. I just like to play with them every now and then.

***

Engineering

Chief Engineer, Montgomery Scott was busy checking and re-checking the systems to make sure that they were in full working order. He needed to reassure himself that the Enterprise was ship-shape and in top order. To that end he was on his way to check that the warp core was purring like a kitten.

As he made his way through engineering, the hairs on the back of his neck suddenly came to attention.

Scotty cautiously turned the corner, and stopped.

Standing at one of the terminals was a humanoid figure.

It appeared to be part human and part machine. More than half its body covered with mechanical implants.

From where he stood Scotty could see that he/she/it was scanning data from the terminal with its ocular implant.

The chief engineer got out his communicator and flipped it open.

“Scotty to Captain Kirk.”

“Yes Scotty.”

“We have an intruder in engineering.”

“On my way.”

*

By the time Kirk, along with Spock, Khan, Molly and a security team arrived, the Borg intruder had moved to another terminal.

“Update Scotty.”

“At the moment it just appears to be scanning our systems.”

Kirk stepped forward and addressed the Borg directly. “What do you want?”

It made no response.

In fact it was difficult to tell if it even registered their existence.

Molly pulled out a tri-corder and began scanning the Borg. But when she made to move closer, Khan placed a firm hand on her shoulder keeping her in place.

She turned, raising an enquiring eyebrow.

“I don’t think it would be advisable to get too close,” he responded. “We have no idea just what type of enhancements their technology gives them.”

“Which was why I was scanning him,” Molly replied.

“Better to be safe than sorry,”

“I agree,” Kirk stepped in. “Ensign stand back.”

Molly immediately complied.

“Captain,” Spock drew everyone’s attention back to what the Borg was doing.

Having scanned a number of systems it now used an implant, where its hand used to be, to try and download information from the terminal.

“Step away from the terminal,” Kirk ordered.

The Borg continued what it was doing, ignoring him.

“I’m ordering you, step away from that terminal.”

The Borg paused, turned and looked directly at Kirk before turning back. It then proceeded to download from the terminal.

Kirk turned to his security chief. He nodded, indicating his permission to engage the intruder. “Set your phaser to stun,” he said.

But to everyone’s surprise stunning the Borg only temporarily slowed it down.

When it returned to its task it seemed even more determined and immediately increased its efforts.

Scotty rushed over to check another terminal as lights all around began to flicker. “It’s draining the ship of power,” he reported.

“Neutralize the intruder,” Kirk ordered. “Use whatever means necessary.”

Security opened fire, their phasers still set to stun.

This time their efforts had no affect at all.

“Fascinating,” Spook commented.

Khan looked on in amazement. “Its adapted to the phaser setting.”

“Set to kill,” Kirk ordered.

This time the Borg fell down dead.

But no sooner had it died then another appeared and took its place at the terminal.

When it continued downloading security opened fire again.

To no avail, the Borg had adapted once again.

Once the download was complete, the Borg disconnected itself from the terminal. It then bent down to its fallen companion and calmly removed specific implants.

Then both were transported off the Enterprise.

Kirk turned to Scotty. “How much power did they drain?”

Scotty checked. He didn’t like what the readings told him. “Enough,” he replied. “All systems, shields etc are at 50%”

Outwardly he appeared calm, but internally Kirk was furious. The Earth had been attacked without provocation. Many that he had trained with had died when they had attempted to defend their home planet. And now his ship had been violated.

“I think we need to return the visit.”

***


	5. In the Belly of the Whale

**Summary for the Chapter:**

> When the Earth is threatened, sworn enemies must work together to defeat a greater foe.
> 
> Disclaimer:  
> I don’t own any of these characters. I just like to play with them every now and then.

***

USS Enterprise NCC-1701

The Bridge

Kirk was never happy being left behind. But he knew that the away team had to be small so as to not attract too much attention. Also with Spock and Khan as part of the team, they were more than adequately covered to deal with whatever situation they were likely to be faced with.

That did not mean that he would not be keeping a close eye on what was going on. Their safety was his top priority.

He turned to his helmsman. “Mr Sulu, if your fix on the away team wavers in the slightest, I want you to beam them back immediately.”

“Yes Captain,” Sulu responded. 

***

The BORG Cube

The away team made up of Spock, Bones, Khan and Molly rematerialised inside the Borg ship.

Though they had all seen a glimpse of the interior when the Borg had contacted them. Seeing the reality up close took everyone’s breath away.

It was so alien.

There was simply no other way to describe it.

They cautiously moved to inspect their surroundings.

All found it disconcerting. There was nothing that they could see or hear that was anything like what they were used to.

There was no humming of engines, no voices, and no audible communications of any kind. If the Borg had not spoken when they had stated their intentions, it would have been reasonable to assume that they communicated telepathically.

As the Enterprises scanners had already indicated the Borg ship had no bridge, no medical bay, no engine room and no crew quarters, or at least none that the away team would recognise as such.

All they could see were compartments, with two Borg in each. That was all the ship appeared to be made up of, row upon row, level upon level. There were hundreds of them, thousands, possibly hundreds of thousands.

A closer inspection of them showed that they were stasis chambers. This realisation revealed a number of interesting areas for hypothesis.

Bones carefully checked one of the Borg in its allotted slot. “Incredible,” he murmured as he read his tri-corders readouts.

“Analysis Doctor,” Spock queried.

“Each chamber appears to be designed for a specific Borg.”

“To what purpose?” Khan asked as he examined a connection port on an uninhabited chamber. “To recharge their batteries,” he mused more to himself than to the others.

At that moment the away team was taken by surprise when a Borg made its way towards them.

When Khan went to reach for his weapon, Molly stopped him. He looked down at her in confusion.

“Wait,” she said.

The Borg completely ignored the away team and made its way to the chamber Khan had been examining and plugged itself in.

The doctor took some more scans before giving an explanation. “Their purpose appears to be a more…collective one.”

Intrigued, Spock walked over to the Doctor and scanned the Borg with his own tri-corder. “I concur with your analysis doctor.”

Khan looked around at his surroundings. The conclusions they were all coming to were simply awe-inspiring. But they left him feeling very uneasy and uncomfortable. “So basically the Borg are powering their ship themselves through their connection via these slots,” he clarified.

“It would appear so,” Spock responded. “Furthermore it would appear that the technology required for this type of interface is far advanced of our own,” he added.

“What are you saying?” Bones asked. “That they’re from the future!”

“We have to consider the possibility doctor. Everything we have observed so far leads to that being the only logical explanation.”

“So how did they get here?” Molly asked.

Spock looked around, his brow furrowed in thought. “It is possible that they may have developed the technology that could allow them to create a wormhole…”

Before they could continue their discussion they all became aware of a noise. One they were not expecting to hear on a ship such as this.

“Was that a…?” Khan started.

“I believe so,” Spock replied.

“But, how?” McCoy asked.

“Only one way to find out,” Khan said as he, followed by Molly made their way towards the unbelievable sound.

*

Khan, Molly, Spock and McCoy all stood completely stunned, none could believe what they were seeing. Inside a specifically designed humidicrib draw was a human baby.

Or at least that was how it had started out.

Spock flipped open his communicator. “Mr Scott.”

“Yes Commander,” Scotty immediately responded.

“Four to beam back.”

***

**Notes for the Chapter:**

> I fully acknowledge that chapters 4 and 5 have been heavily influenced by the ST:NG episode, Q Who?. It is in part because of this that it has taken me so long to upload the next chapter. A case of overthinking things.


	6. A Difference of Opinion

**Summary for the Chapter:**

> Disclaimer:  
> I don’t own any of these characters. I just like to play with them every now and then.

***

Conference Room

The discussion to decide how best to deal with the Borg had quickly descended into a heated argument between Kirk and Khan.

The others in the room had sensibly decided to stand back and allow the two titans to battle it out.

“You cannot negotiate with them Captain,” Khan argued. “They’re not interested in anything you have to say.”

“They are sentient beings and therefore they must be given due consideration,” Kirk countered.

Khan knew Kirk was doing his best to temper his usual gung ho attitude and attempting to take a more measured approach, more befitting of a Starfleet Captain. But really there was a time and a place, and that most definitely was not now.

“Due consideration? Kirk have you forgotten their demands when they first communicated with us. They don’t wish to be friends, or allies. Their only intention is to conquer, and given their advanced technological capabilities that wont be difficult to achieve.”

“You sound as though you admire them,” Kirk noted sourly. “Though I suppose I shouldn’t be so surprised, given the similarities between you,” he taunted.

Khan looked momentarily stunned at the implied accusation, but he quickly recovered himself.

“You were the one who brought me into this situation Captain. You did so for the exact same reason that Admiral Marcus revived me. You need my superior intellect, my savagery to defeat an alien threat that has attacked the Earth for no known reason, other than that they can.”

Kirk blanched at the mention of Admiral Marcus’ name. It was clear from the knowing smirk on Khan’s face that that had been his intention.

“I did not bring you here to destroy them.”

“Then you’re a fool,” and with that Khan turned and left the room.

Kirk was furious. To be put down in front of his senior officers was intolerable. And it didn’t help that deep down he knew that just about everything Khan had stated was true.

He desperately needed to take his anger out on someone.

He chose Ensign Hooper.

As she moved to follow Khan, he intercepted her.

“Ensign, I thought I’d made my orders clear. You were to keep Khan under control.”

If Molly was supposed to be intimidated by his stance she showed little sign of it. “Even when everything he said was right?” she queried.

The Captain, and everyone else in the room looked at her with a mixture of surprise and admiration.

“At the very least,” she continued. “Do him the courtesy you would of anyone else in this room and at least consider what he suggests. Don’t dismiss them outright because Khan is the one who has made them.”

“That’s not…” Kirk began, but he knew he was on shaky ground.

“Really?” Molly queried as she headed out of the room intent on finding Khan. “Prove it.”

***


	7. A Moments Peace

**Summary for the Chapter:**

> Disclaimer:  
> I don’t own any of these characters. I just like to play with them every now and then.

***

Observation Deck

She found him on the observation deck looking sightlessly out the window. His spine rigidly straight, arms folded across his broad chest, legs slightly splayed. Khan’s posture spoke volumes, of his anger, frustration, hurt, and… 

His loneliness.

Molly paused, uncertain what she could offer him in the face of such powerful and conflicting emotions.

He was a man out of time. Completely out of sync with everything around him. He had no one to confide in. No one who understood how he felt, or cared about what had been done to him, what he had been forced to endure for the sake of his crew since their ship had been discovered drifting in Federation space.

Was it any wonder that he was now so defensive? He had been physically altered without his permission, and his memories modified. When his augmented DNA had reinstated his memories he’d still been unable to obtain any justice. Instead he’d been further manipulated by Marcus to do his bidding, being threatened with never seeing his crew ever again if he didn’t.

She watched his stance change as he become aware of her presence. His gaze met hers in the windows reflection. Bravely she returned his gaze before slowly approaching him.

“He’s nothing like Admiral Marcus,” she began.

Khan looked down at the small woman at his side, and raised an inquiring eyebrow, his expression sceptical.

“He’s brash and hotheaded I grant you,” she continued. “But he would never use anyone the way Admiral Marcus treated you. There are few in Starfleet who would.”

Khan gave a derisive snort.

“Do you know why Kirk chose you?” he asked.

The question took her by surprise. After a moment’s thought she responded. “Because I like you,” she said, blushing prettily.

“Oh if only that were so,” Khan’s deep voice rumbled in wistful amusement.

When Molly opened her mouth to reply, Khan forestalled her by gently placing a finger against her lips and shaking his head.

“No Molly. The reason your captain chose you was because he remembered when I was first brought on board the Enterprise. As soon as I saw you I couldn’t keep my eyes off you.”

Molly’s eyes widened so delightfully at his confession, that he couldn’t contain the smile that spread across his face. But only for a moment, he needed to make her understand.

Taking her upturned face in his hands Khan continued his explanation. “I’m not a nice man Molly Hooper, I have done many terrible things.” He paused, his mind focussed on memories from his distant past through to his futuristic present. He looked deep into her big brown expressive eyes and said with a sigh. “I regret some of what I have done and been accused of, but from where I stood I could see no other alternative.”

Molly nodded her understanding. By the time Khan’s trial had come to an end, and all that Admiral Marcus had done in his attempts to turn Starfleet into a militarised organization had been revealed. There were few that did not feel some sympathy for the Augment who had been so cruelly used as a means to an end. 

The timber of Khan’s voice deepened as he admitted. “I took one look at you, and I wanted you. You were something pure and innocent, and I knew I had to have you… body and soul.”

Molly trembled in response to his ardent declaration.

“Kirk saw it, and now he’s using it as a means to keep me under control. He knows I would be willing to do anything to have the opportunity to earn the right to be with you if I can.”

Molly observed Khan’s tortured expression. She read his longing for freedom, to begin a new life, one that might even include her, if she so chose.

Reaching up she brought his face down until it was level with hers. “We all have the capacity to be good or bad, depending on the choices we make. You’ve made some bad decisions, but I refuse to believe that they define you. Nor do I think the Captain believes that of you either. If he did, he could never justify placing me in harms way. So, we’ll help him, Starfleet, the Federation and the Earth’s population to rid our solar system of the Borg. And then maybe your case can be reviewed, and they may be willing to see you in a more favourable light.”

She released her hold on him and stepped back.

As they existed the observation deck, Molly added. “I will help you all I can Khan, but be warned, I am no ones fool. I wont do anything to jeopardise or betray the Enterprise’s crew. Do I make myself clear?”

Khan looked at her with admiration. The more he got to know Molly Hooper, the more he willingly fell under her spell. Without hesitation he readily agreed to her terms.

***


	8. Making Plans

**Summary for the Chapter:**

> Disclaimer:  
> I don’t own any of these characters. I just like to play with them every now and then.

***

The Bridge

When Khan and Molly exited the turbo lift onto the Enterprises Bridge, it was clear that the debate over what needed to be done had already begun.

They made their way over to the group standing around the Captain’s chair.

Not surprisingly Mister Spock and Doctor McCoy were in the middle of a heated, at least on the doctors side, discussion.

“Given that they appear to be connected together in a hive mind, we must consider the possibility that they’re communicating with others of their kind across space-time.” Spock stated.

“Now there’s a cheery thought,” Bones muttered under his breath.

Spock turned, one eyebrow raised. “Problem Doctor?”

McCoy let out an exasperated sigh. “I just think we’re dealing with enough as it is at the moment. These Borg are clearly the most dangerous species we’ve so far encountered.”

“Your point Doctor?” Spock enquired patiently.

“My point, you pointy-eared bastard is that this crew is dealing with enough as it is at the moment. If you destroy their hope completely, they’ll feel there’s little point in fighting.”

“Agreed,” Kirk interrupted, bringing their bickering to a premature end. “But the question still remains, what can we do to defeat them?”

“If I might make an observation?” Khan requested.

Kirk nodded.

“If the Borg do possess a collective consciousness, then our best chance of defeating them is to take them by surprise.”

“What did you have in mind?” the captain asked, genuinely curious.

“We need to do something they’re not expecting.”

“Like what?” McCoy demanded, waving his arm to vaguely indicate the debris that appeared through the view-screen. “From the wreckage out there I’d say that a number of options were tried. All of which failed I might add.”

Khan gave himself time to consider his words before replying.

“While we were aboard their ship they did nothing to hinder us, even though we were clearly armed.”

Spock saw where the augment was going. “They didn’t view us as a threat.”

Khan nodded. “Correct. If an away team could board their ship with a number of small devices…”

“Explosives?” Kirk queried.

Khan shook his head. “A weapon of that type, no matter how small would be easily detected.”

“What then?”

“What about a device that when activated, only incapacitates?”

Spock looked sceptical. “Surely the Borg would adapt too quickly for them to be effective.”

“Not necessarily,” Khan argued. “If it’s something they’ve never come across before, thereby not expecting, it could work as a diversion. They will adapt to it, but it may give us enough time to get our real weapon up and running.”

Khan’s plan certainly seemed feasible. “What weapon do you have in mind?” Kirk asked.

“Red Matter.”

The hope that was building up in everyone involved in the discussion immediately died.

“It’s all gone,” Kirk said.

“Something else that came from our future,” McCoy added dourly.

But Khan refused to be defeated so easily. “The one who brought the Red Matter into the past is still alive is he not?”

Everyone nodded.

“Then surely we can ask him how we can create it, or something like it.”

“For that we would require knowledge of technologies far beyond our capabilities,” Spock pointed out.

“Then allow Ambassador Spock and I to discuss the matter,” Khan responded. “I’m certain between the pair of us we can come up with a solution.”

Kirk turned to Uhura. “Make contact with Ambassador Spock on New Vulcan.”

“Yes Captain,” she responded.

“In the meantime,” Khan continued. “We need to get to work on a diversion. Mister Scott, I believe I’ll need your assistance.”

 

Engineering 

When Khan and Scotty presented their devices to the other senior crew, their response was more sceptical than impressed.

“Are you certain they will work?” McCoy asked. “They look too simple, so primitive.”

“That’s the beauty of them,” Scotty responded with his usual enthusiasm. “They appear totally non-threatening.”

“And as such the Borg should totally ignore them,” Khan explained. “Only when they’re activated will they realise their mistake. By that time they will be temporarily out of commission. Hopefully long enough for us to get the second part of our plan into motion.”

Kirk had no idea if this crazy plan would work, but really what choice did they have.

“Well let’s hope it works,” he said. “Because we wont get a second chance at this.”

***


	9. Plan Into Action

**Summary for the Chapter:**

> Disclaimer:  
> I don’t own any of these characters. I just like to play with them every now and then.

***

Engineering

“You don’t have all the components to replicate it,” Ambassador Spock warned.

“Well I’ll just have to do the best I can with what we have,” Khan responded. But as he made to end the transmission, Ambassador Spock waylaid him.

“Khan.”

“Yes, Ambassador,” Khan replied calmly. He was impatient to start work on recreating the Red Matter. The clock was ticking and he didn’t have time for pleasantries.

Ambassador Spock held up his hand, giving the familiar Vulcan salute. “Good luck.”

“Thank you Ambassador.”

With a raised eyebrow the Ambassador added. “You will need it.”

Noting the Vulcan’s expression, Khan muttered none too softly. “A Vulcan with a sense of humour, just what I need.”

*

But the Ambassador’s warning kept reverberating in the back of his mind.

Red Matter was a highly volatile substance at the best of times. Attempting to replicate it knowing you don’t have all the correct ingredients and with no time to test how it would react, was simply a disaster waiting to happen.

Then again, what choice did they have?

The safety of not only the Earth but also that of all quadrants of the Federation could well be in jeopardy if they didn’t attempt it.

Khan knew that with his genetically altered DNA that he was far superior to many around him. But when he looked at the Borg and their way of adapting and improving their knowledge using assimilation and artificial components, it churned his stomach and left him determined to halt their progress in this star system before it could begin.

“Mr Scott,” Khan got the attention of the Chief Engineer as he made his way over to him. “I believe our plan may need a few adjustments.”

*

The Bridge

Kirk, Spock, and Bones looked rightly concerned when Khan and Scotty explained what they had done.

“Let me see if I understand you correctly,” Kirk chose his words carefully as he looked at the cylindrical container in the augment’s hands. “You have now placed Red Matter within the device that is to incapacitate the Borg.”

“Correct,” Khan replied.

“To what purpose?” Commander Spock queried.

“To use a quaint old Earth saying,” came back the response. “We are going to ‘kill two birds with one stone.’”

When all he received was perplexed expressions, Khan went on to explain. “This device contains two timers, the first will activate the Rankine nullifier, which will temporarily incapacitate the Borg. A second timer will go off five minutes later, releasing the Red Matter, if it works as it should, then the Borg ship should rapidly become crushed as it morphs into a Black Hole.”

With no other option Kirk had little choice but agree to the mad plan.

“So, now what?” he asked.

“Given the completely unpredictable nature of the Red Matter we have created, I feel it only right that I be the one to transport across to the Borg ship…” Khan began.

“No,” Kirk stated firmly.

“But, Captain…”

“You’re gonna need help,” Scotty pointed out. “We’ve made six devices, and as you say all are unstable and unpredictable. So I’ll be coming with you.”

“As will I,” Spock announced. Responding to the surprised look on the augments face, he responded with his typical logic. “With three of us, we can place the six devices in the most strategic positions more efficiently.”

“And the quicker we get them placed, the faster we can get outta there,” Scotty added.

Feeling more relieved with the plan, Kirk finally gave Khan the go ahead.

***

The Borg Ship

When the away team first transported to the Borg ship there had been little movement. The same could not be said this time.

Though the Borg continued to ignore the intruders, they themselves were far more active, with the away team having to constantly weave and dodge around the ever-increasing number of Borg as they made their way around the ship.

“I don’t like this,” Scotty said, having to once again move out of the way of some oncoming Borg.

“It would appear they too are getting ready for some plan of action,” Spock noted.

“Then gentlemen,” Khan stated. “ I suggest we get these devices placed as quickly as possible.”

“Agreed,” Spock and Scotty answered together.

***

Enterprise Bridge

“Are they back on board?” Kirk asked.

“Affirmative Captain,” Chekov responded.

With the away team safely back aboard, there was only one thing left to do.

“Okay Mr Sulu,” Kirk instructed his helmsman. “Time to get their attention.”

“Yes Captain,” Sulu responded.

“Fire!”

***

**Notes for the Chapter:**

> Hope to have another chapter uploaded in a couple of days.


	10. David and Goliath

**Summary for the Chapter:**

> Disclaimer   
> I don’t own any of these characters. I just like to play with them every now and then.

***

The shielding on the Borg vessel was far superior and easily deflected the Enterprise’s phaser strikes, which were likely regarded as nothing more than an irritation.

But it was enough to get the Borg’s attention.

Their response was immediate. 

*

Enterprise Bridge

The Enterprise was suddenly rocked as if struck by a large asteroid, and the exterior hull began to shudder.

Sulu checked the readings appearing on his terminal. “Captain,” he exclaimed. “They’ve locked on to us with a tractor beam.”

“Go to warp,” Kirk instructed.

Sulu attempted to do as ordered once, twice, three times. But it was all in vain. “We can’t Captain.”

Kirk spoke into the communicator in the armrest of his chair. “Kirk to Engineering. Khan, how long until the Rankine nullifier is activated?”

*

Engineering

Khan glanced over at the timer he’d set up at his station. “Any second now Captain.”

*

The Bridge

No sooner had the words left the augment’s mouth, than the tractor beam became disengaged.

Kirk gave his next order to his helmsman. “Go to warp Mr Sulu.”

***

The Borg Ship

Everything inside the cubed vessel was frozen into motionlessness. The ice-like material clung to every inch of the ship and to the many thousands of individuals that manned it.

But within a couple of minutes movement was detected. And shortly after that, the ship was once again fully functional.

Though the expression on the Borg’s faces showed complete indifference to what had happened, their actions showed an unwillingness to be beaten by a race they had initially believed to be inferior.

The actions of the individuals aboard that one small ship however had shown that they were clearly a race with surprisingly unexpected resourcefulness.

And they would therefore be of great benefit to the Collective.

It did not take the Borg long to discover where the ship had warped to, and they set off in pursuit.

*** 

The Enterprise re-emerged into an area of space already proven to be uninhabited. And it was here that they waited for the Borg to follow.

They didn’t have long to wait. The Borg ship soon loomed into view.

*

Enterprise Bridge

The atmosphere on the Bridge was tense, a mixture of anticipation and dread, in equal measure.

The view on the Bridge’s view screen suddenly changed from an external view of the ship to an internal one, and as before all that could be seen was deck upon deck of compartments, where the Borg stood connected to the ship.

And as before they spoke as one. “Resistance is useless. You will be assimilated. Resistance is futile.”

*

Engineering

Scotty and Khan could hear the Borg’s transmission as it was being broadcast ship-wide, but their focus remained on the countdown of the timer to the second device containing the Red Matter.

“Three… Two… One…”

***

The Borg Ship

The remaining half of the six cylinders exploded, releasing a number of what appeared to be inconsequential red droplets.

The droplets drifted aimlessly around the ship, completely harmless, until they began to bump and collide into various parts of the ship.

A number of Borg paused, something was wrong. The ships systems were failings, as was its structural integrity.

***

Enterprise Bridge

The Borg’s transmission came to abrupt end.

Kirk allowed himself the luxury of a well-satisfied grin. The plan had worked.

“All right Sulu, I think its time we headed home.”

*

Engineering

Khan and Scotty were also looking very pleased with themselves, but their grins were quickly wiped from their faces when the ship jolted abruptly, and to their horror it was dragged forcibly towards the Borg ship.

“That can’t be good,” Scotty noted, stating the obvious.

*

The Bridge

“Is it their tractor beam?” Kirk asked, hopeful that it was so.

“Negative,” came Sulu’s reply.

“Can we go to warp?” Kirk knew the answer, but felt compelled to ask.

“No Captain.”

Kirk and Spock exchanged knowing looks. Kirk shrugged his shoulders. “It was worth a shot.”

*

Engineering

Scotty remembered the last time the Enterprise had been caught up in a Red Matter created Black Hole, and he’d sworn then that he’d never allow the Enterprise to be put through such a situation again.

And yet here they were. He winced as he heard the creaking of the outer hull and observed the cracks that were sprouting up all over the place as the ship began to go through her death throes as she was drawn back into the all consuming void that the Black Hole was creating.

The sheer force of this Black Hole was far and away more intense than what they had faced before. And if he were honest with himself he wasn’t certain his solution of ejecting the warp core and then detonating it would be enough this time to get them out of their current fix.

What they needed now was a miracle.

Khan had not been idle. As soon at the Enterprise had become ensnared he began looking for possible options. He was aware of Mr Scott’s solution the last time the Enterprise had faced such a situation, and had been extremely impressed by it. But the situation they were facing this time was far graver, and the solution needed was also going to require an extra special kick.

And then he had it.

“Of course,” he murmured, his gaze wandering up and down the dilithium chamber.

*

The Bridge

In desperation Kirk contacted Engineering. “Scotty please tell me you’ve found a solution to get us out of this?”

“We’re working on it Captain,” was not the reassuring response he was hoping for. 

“Then work harder,” Kirk ordered. “We’re running out of time.”

“Understood.”

*

Engineering

Scotty looked at the augment like he’d finally lost the plot completely. “You can’t be serious,” he said.

“Increasing the matter/antimatter reaction in the dilithium chamber will give the warp core a super charged boost when it’s ejected. Then when its detonated, the force should push us clear of the Black Hole. You know it will, you’ve done it before.”

“But to increase the reaction would require direct contact with the crystals, which raises the risk of exposure to radiation.”

“Yes, I know. That’s why I’ll be the one to do it.”

“Are you certain your body can handle the potential radiation that the crystals may release?”

“It’s a risk I’m prepared to take.”

“No,” came the distressed cry. Molly had just entered Engineering in time to hear Khan’s statement.

Not daring to look her in the eye, in case her expression weakened his resolve, Khan strode with determined steps towards the chamber. Molly made an attempt to stop him. But Scotty pulled her back.

His expression grave, as he shook his head. “No lass. Let him try, it may be our only hope.”

***

**Notes for the Chapter:**

> I fully acknowledge that my knowledge about Dilithium Crystals and how they work etc. is close to nil. Therefore any errors in my explanations are completely my own, and I take full responsibility for them.


	11. From the Ashes

**Summary for the Chapter:**

> Disclaimer:  
> I don’t own any of these characters. I just like to play with them every now and then.

***

The Black Hole continued to expand, consuming all matter that was caught up in its destructive mass.

Nothing could escape its pull.

Almost nothing….

A soundless flash before an object was ejected from the Black Hole’s very core as if hurled by an enormous slingshot.

The object spun out of control, its momentum only returning to something approaching normal when it was finally free of the dark matters deadly grip.

The Enterprise was free. The ship’s outer hull had taken a real beating, and internally things weren’t much better. But for all that, they had just enough power to enable them to limp back to Earth at impulse speed.

*

The Enterprise - Engineering

When Khan finally emerged from the dilithium chamber, he was greeted with a jubilant “Ya bloody did it, ya mad bastard,” before Scotty enthusiastically thumped the augment on the back.

When Molly flung herself into his arms, Khan’s exhausted limbs crumbled, spilling them both to the floor. Pulling Molly securely into his embrace, Khan let a smile play upon his lips as he lost himself in the delightful sound of Molly, laughing and crying with relief.

But as his strength returned, his thoughts turned to the rest of the Enterprise crew. “How bad is the damage?” he asked, as he observed Scotty attempting to ascertain the damage with only limited data available.

“It’s bad,” Scotty finally admitted. “But it could’ve been worse…”

Khan nodded in subdued acknowledgement, accepting Molly’s comforting embrace as she wrapped her arms around him and laid her head against his shoulder, offering solace and support. 

*

The Bridge

Damage and casualty reports were coming intermittently from all over the ship. But the one area that so far had not reported in was engineering, and that had Kirk worried.

“Scotty! Khan! Is everyone all right there?”

There was an agonising pause as the ship’s damaged systems attempted to re-establish internal communications. Until finally. “All’s fine here Captain,” The Chief Engineer assured him.

Kirk gave an audible sigh of relief, before giving Sulu one last order. “Take us home Mr Sulu.”

***

The Borg Ship

In the final death throes before succumbing to complete annihilation, one final report was sent to the far reaches of the Delta Quadrant, to the Borg’s central base at Unicomplex.

What it contained, and whether it was received is unknown. 

***

**Notes for the Chapter:**

> Well we're coming to the end, of this story at least. :-) The final chapter has been completed and will be updated within the next 24 hours, probably sooner.
> 
> Thank you all for your lovely support, keep those kudos and comments rolling in. :-)


	12. Epilogue

**Summary for the Chapter:**

> Disclaimer:  
> I don’t own any of these characters. I just like to play with them every now and then.

***

Starfleet Headquarters – San Francisco

In light of Khan’s contribution to the repelling of the threat that the Borg had posed, no opposition was raised when Captain Kirk made a request for a retrial.

Though the attempted destruction of Starfleet Headquarters could not be overlooked, the late Admiral Marcus’ manipulations of Khan, was now given due consideration. For it is certain that had the Admiral lived, he would have been charged with war crimes, and probably more.

Then the senior members of the Enterprise crew gave their statements. But by far the most compelling was the statement, and insights made by Admiral Spock, who laid before the Tribunal his knowledge of the Khan Noonien Singh that he knew in his timeline, before giving a comparison based on his thoughts having now had the opportunity to interact with the Khan Noonien Singh of this altered timeline. He spoke eloquently of the decisions made by the augment that led to events for which Khan was originally charged, challenging judge and jury to place themselves in Khan’s position and asking if they would have acted any differently?

In the end Khan’s original charges and sentence were downgraded, and he was released into the custody of the Enterprise’s Captain.

*

Celebrations were in full swing. Celebrating not only the decision of the tribunal, but also their survival, when so many others had not been so lucky when they'd attempted to take on what was clearly the most powerful beings Starfleet and the Federation had ever encountered.

Everyone looked happy and relaxed, though there was one who stood back, preferring to observe the proceedings in quiet contemplation.

Kirk watched Khan closely. But this was a Khan many had never seen before, smiling and relaxed, though Kirk was certain that the young ensign at his side had a large part to play in his transformation.

Kirk himself remained troubled, as there was still the matter of the information he’d withheld from Khan. Information the augment had every right to know. 

As if he sensed the intense observation he was under, Khan turned away from the festivities and headed over to the Captain.

“You look troubled Captain, something on your mind?”

It was now or never.

“Actually yes,” Kirk began. “It concerns your crew…”

When he’d finished his explanation he observed the augment’s reaction, noting deep sadness and pain, that his crew were again lost, but sensing no animosity towards himself and his crew. 

“We will do all we can to assist you in finding out who has your crew and where they are being held,” Kirk earnestly assured Khan.

“I think you will find Captain that the where is the more important question,” Khan responded after much thought. “For I believe I already know who has possession of them.”

“You do”

“Oh yes,” he replied bitterly. “There is only one organization ruthless and arrogant enough to undertake such an audacious plan of action with the means to conceal their movements. I know them all too well. These actions bare the unmistakable stain that is Section 31.”

***

**Notes for the Chapter:**

> Work has already begun on the follow up to this story.
> 
> Title: Section 31  
> Summary: It is said that ‘Power corrupts, and absolute power corrupts absolutely.’  
> Or to put it another way: ‘Welcome to Section 31’  
> Rated: Mature

**Author's Note:**

> Kudos and Comments most welcome.


End file.
